-THe only thing I can narrow to this problem is when I modified the rain effect, and changing the FX file for the map..... But, It still has this problem when I just get rid of either one..... So, is it just freaking out, and do I have to redo this map?
Try cleaning and munging. Copy the default rain fx/sky files (whatever you think might pertain that you edited prior to this problem) and put them where they belong (maybe make backups of your edited versions, unless the changes are simple), then clean all, and munge.
You shouldn't have to redo the map under any circumstances, with this sort of issue, as I doubt its just..borked.
Also, this might be way out in left field, but you sure its not gfx card related? some of the tearing/artifacts in the visible portions of the map look awefully like video card issues.
unless you munge a new common.lvl and shell that won't work. copy the effect over to your worlds effect folder and then change the name of it and in the sky file change it to the new name.
as for the glow problem you had, did you edit the sky .tga? some skys (like yavin) have glow and if you remove the alpha channel then the sky will just be white/yellow and glow.